--- a/compleasm.xml	Wed Feb 14 14:31:44 2024 +0000
+++ b/compleasm.xml	Tue Mar 12 09:59:05 2024 +0000
@@ -7,11 +7,16 @@
         <requirement type="package" version="@TOOL_VERSION@">compleasm</requirement>
     </requirements>
     <command><![CDATA[
+    
+    mkdir -p galaxy_db &&
+    cp -r '${busco_database.fields.path}/lineages/${lineage_dataset}/' 'galaxy_db/' &&
+
     compleasm run
     -a '$input'
-    -o galaxy
+    -o galaxy_output
     --mode $mode
-    -l '$busco_database'
+    -L 'galaxy_db'
+    -l '$lineage_dataset'
 
     #if str($specified_contigs) != '':
         --specified_contigs '$specified_contigs'
@@ -44,21 +49,25 @@
         <param name="busco_database" label="Choose the BUSCO database to be used" type="select" multiple="false">
             <options from_data_table="busco_database"/>
         </param>
+
+        <param name="lineage_dataset" type="select" label="Lineage">
+            <expand macro="lineages"/>
+        </param>
     </inputs>
 
     <outputs>
-        <data name='full_table_busco' format='tsv' label="${tool.name} on ${on_string}: full table BUSCO" from_work_dir="galaxy/*_odb10/full_table_busco_format.tsv">
+        <data name='full_table_busco' format='tsv' label="${tool.name} on ${on_string}: full table BUSCO" from_work_dir="galaxy_output/*_odb10/full_table_busco_format.tsv">
             <filter>outputs and 'full_table_busco' in outputs</filter>
         </data>
-        <data name='full_table' format='tsv' label="${tool.name} on ${on_string}: full table" from_work_dir="galaxy/*_odb10/full_table.tsv">
+        <data name='full_table' format='tsv' label="${tool.name} on ${on_string}: full table" from_work_dir="galaxy_output/*_odb10/full_table.tsv">
             <filter>outputs and 'full_table' in outputs</filter>
         </data>
-        <data name='miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="galaxy/*_odb10/miniprot_output.gff">
+        <data name='miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="galaxy_output/*_odb10/miniprot_output.gff">
             <filter>outputs and 'miniprot' in outputs</filter>
         </data>
-        <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy/*_odb10/translated_protein.fasta">
+        <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy_output/*_odb10/translated_protein.fasta">
             <filter>outputs and 'translated_protein' in outputs</filter>
-        </data>              
+        </data>             
     </outputs>
 
     <tests>
@@ -66,7 +75,8 @@
             <param name="input" value="small_genome.fasta"/>
             <param name="mode" value="busco"/>
             <param name="outputs" value="full_table_busco,full_table,miniprot,translated_protein"/>
-            <param name="busco_database" value="eukaryota"/>
+            <param name="busco_database" value="eukaryota_odb10"/>
+            <param name="lineage_dataset" value="eukaryota_odb10"/>
             <output name="full_table_busco">
                 <assert_contents>
                     <has_text text="Busco id"/>